Well, this certainly explains a whole lot. Both Apple and Microsoft have stated that the legality of Theora is highly debatable, and as it turns out, they knew more than we do - most likely courtesy of their close involvement with the MPEG-LA. Responding to an email from Free Software Foundation Europe activist Hugo Roy, Steve Jobs has stated that a patent pool is being assembled to go after Theora. Update: Monty Montgomery of Xiph (Ogg and Theora's parent organisation) has responded on Slashdot: "If Jobs's email is genuine, this is a powerful public gaffe ('All video codecs are covered by patents'). He'd be confirming MPEG's assertion in plain language anyone can understand. It would only strengthen the pushback against software patents and add to Apple's increasing PR mess. Macbooks and iPads may be pretty sweet, but creative individuals don't really like to give their business to jackbooted thugs."

But it is quite likely that any patents being violated have overly broad claims.

Overly broad claims are just standard practice for any patent.

Of course, by the time the court cases to actually decide are finished, the patents will have expired anyway.

All patents make overly broad claims, but when it comes to the crunch the are judged ONLY on the very specific claims.

Microsoft's FAT patents are classic. It turns out that the specific claims are not for FAT (which is not Microsoft's invention anyway), but rather, for Long File Names (LFN) stored on a FAT filesystem. Even more specifically, the patents are awarded based on Microsoft's claim to have invented a novel method of storing BOTH a LFN and a short (8.3) filename for each file at the same time.

So, to avoid this patent, all that has to be done is to fail to store both a LFN and a SFN. Either one or the other for any given file, but never both. This way, your FAT LFN-compatible software still does not violate the specific claim.

Just avoid the claimed specific methods and you don't infringe the patent.

The LFN storage technique however was ingenious. It is not an overly broad technique.

Long File Names (LFN) are stored on a FAT file system using a trick—adding (possibly multiple) additional entries into the directory before the normal file entry. The additional entries are marked with the Volume Label, System, Hidden, and Read Only attributes (yielding 0x0F), which is a combination that is not expected in the MS-DOS environment, and therefore ignored by MS-DOS programs and third-party utilities. Notably, a directory containing only volume labels is considered as empty and is allowed to be deleted; such a situation appears if files created with long names are deleted from plain DOS.
From http://en.wikipedia.org/wiki/File_Allocation_Table